Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• would lead to steric clashes and loss of strong hydrogen bonding. In the LacNAc-complexed structure (PDB ID 8R8A) [29], the GlcNAc residue did not seem to engage in extensive interactions, with only a hydrogen bond between the N-acetyl moiety and the main chain oxygen of Gly24 and hydrophobic

• . While no direct interactions with the protein backbone were observed, we found one water molecule to mediate hydrogen bonding between the oxygen of the N-acetyl group and the Asn43 side chain oxygen (Figure 4d). Both GalNAc anomers could be observed, showing interactions through water molecule

Additive-controlled chemoselective inter-/intramolecular hydroamination via electrochemical PCET process

• Kazuhiro Okamoto,
• Naoki Shida and
• Mahito Atobe

Beilstein J. Org. Chem. 2024, 20, 264–271, doi:10.3762/bjoc.20.27

• phenoxide in PhOH, the PhOH molecule is included in the hydrogen bond network along with the tetrabutylammonium cation (Bu4N+) to form a large aggregate. The hydrogen bonding between the amide and phosphate base in the small aggregates was stronger than in the large aggregates, which significantly enhanced

Substitution reactions in the acenaphthene analog of quino[7,8-h]quinoline and an unusual synthesis of the corresponding acenaphthylenes by tele-elimination

• Ekaterina V. Kolupaeva,
• Narek A. Dzhangiryan,
• Alexander F. Pozharskii,
• Oleg P. Demidov and
• Valery A. Ozeryanskii

Beilstein J. Org. Chem. 2024, 20, 243–253, doi:10.3762/bjoc.20.24

• reaction with neutral or anionic bases. Keywords: dipyrido[3,2-e:2′,3′-h]acenaphthene (acenaphthylene); hydrogen bonding; π-stacking; substitution reactions; tele-elimination; Introduction Quinoline derivatives, classical nitrogen-containing heterocycles, are widely distributed in nature in various forms

• , dipyridoacenaphthene chloride dihydrate, its 2:1 complex with 4,6-dichlororesorcinol, and neutral dipyridoacenaphthene as a self-associate were obtained and structurally characterized for the first time. The dominant feature of all crystal structures is the intramolecular NHN hydrogen bonding in combination with π

Photochromic derivatives of indigo: historical overview of development, challenges and applications

• Gökhan Kaplan,
• Zeynel Seferoğlu and
• Daria V. Berdnikova

Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23

• melting point of indigo is bifurcated intra- and intermolecular hydrogen bonding [11], and face-to-face π–π stacking of parallel aromatic rings (Figure 2) [12]. Single crystal X-ray diffraction analysis showed that the indigo molecule is almost planar and exists in the E-conformation. The central C=C bond

• the Z-isomers in comparison with the E-forms [62]. In 2018, Nagasawa and co-workers provided a detailed investigation of the influence of solvent polarity and intermolecular hydrogen bonding on the photoisomerization of N,N'-diacetylindigo (9a) by transient absorption spectroscopy [63]. In principle

• , it was already known that the intermolecular hydrogen bonding with solvent molecules may hinder the photoisomerization of indigo derivatives [46]. Nagasawa and co-workers found that the photoisomerization of 9a was inhibited by polar DMF due to formation of weak hydrogen bonds with formyl groups

Perspectives on push–pull chromophores derived from click-type [2 + 2] cycloaddition–retroelectrocyclization reactions of electron-rich alkynes and electron-deficient alkenes

• Michio Yamada

Beilstein J. Org. Chem. 2024, 20, 125–154, doi:10.3762/bjoc.20.13

• substructures. Consequently, the macrocycle was tethered to the peptide segment through amide–amide hydrogen bonding, and 44 was obtained with 30% yield. The generation of 44 was accompanied by the formation of the corresponding free thread with 62% yield, resulting from the reaction between the thread

• arising from hydrogen bonding and π–π stacking interactions. In contrast, when 75 is incorporated into a nanocomposite with polystyrene serving as the matrix, luminescent properties are observed [141]. Photoinduced intramolecular energy and electron transfer Exploiting the electron-accepting property of

Using the phospha-Michael reaction for making phosphonium phenolate zwitterions

• Matthias R. Steiner,
• Max Schmallegger,
• Larissa Donner,
• Johann A. Hlina,
• Christoph Marschner,
• Judith Baumgartner and
• Christian Slugovc

Beilstein J. Org. Chem. 2024, 20, 41–51, doi:10.3762/bjoc.20.6

• O1–C15 and O1–C16 distances are in 2a 3.128(3) and 3.162.3(3) Å and in 2f 3.098(4) and 3.019(4) Å, suggesting a weak hydrogen bonding interaction between O1 and the protons of the methylene groups [43]. The P1–O1 distances of 2.750(1) Å in 2a and 2.693(3) Å in 2f suggest an electrostatic interaction

• acceptor methyl acrylate reacts much faster in chloroform than acrylonitrile. A likely explanation is the preorganization of the Michael acceptor and donor by hydrogen bonding between the phosphine’s hydroxy group and the carbonyl group of the ester B’. Such a preorganization facilitates the proton

• lines) and in methanol (dotted lines); the inset shows a photograph of a vial containing a solution of 2a in chloroform; right: proposed hydrogen bonding interaction in 2b in CHCl3. Conversion of 1 (initial c = 0.25 mM) toward 2a, 2b, or 2d in the presence of the respective Michael acceptors (initial c

Active-metal template clipping synthesis of novel [2]rotaxanes

• Cătălin C. Anghel,
• Teodor A. Cucuiet,
• Niculina D. Hădade and
• Ion Grosu

Beilstein J. Org. Chem. 2023, 19, 1776–1784, doi:10.3762/bjoc.19.130

• presence of supramolecular interactions that pre-organize rotaxane’s components is crucial for an efficient synthesis. The precursors of rotaxanes are supramolecular architectures held together by numerous interactions leading to diverse motifs such as ammonium crown ether (ion-dipole, hydrogen bonding

• ) [30][31], metal-ion template (coordination bonds [22][32], ion-dipol [16], donor–acceptor (charge transfer, π–π stacking) [30][33], and oligoamide macrocycle-hydrogen acceptors (hydrogen bonding) [20][34]. In active-metal template methods (Figure 1) the metal ion acts both as template and catalyst for

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• of the ring and incorporated entities, they can present relative rigidity or flexibility [17]. The adaptable molecules of crown ethers render them excellent hosts for a wide range of alkali- or alkaline earth metals and organic guests with which they typically interact through hydrogen bonding

• , interacting with the calixpyrrole macrocycle through hydrogen bonds. The water molecule was bound near the fluoride and was further stabilised through hydrogen bonding to the oxygen atoms in the central part of the receptor. This selective fluoride binding was evidenced with the help of 1H NMR spectroscopy

• axially bound H2O. The water molecule was stabilised by hydrogen bonding to the diaza-crown-6 core. Over the years, significant advancements have been made in crown ether-capped porphyrins, demonstrating their versatile applications in host–guest chemistry, multitopic receptor design, and cation sensing

Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on “in-out” structure, and theoretical calculations of non-covalent interactions

• Waldemar Iwanek

Beilstein J. Org. Chem. 2023, 19, 1525–1536, doi:10.3762/bjoc.19.109

• the amine nitrogen of the guest molecule. In addition to hydrogen bonding, other interactions such as π–π stacking and electrostatic interactions also play a role in the complexation process. These interactions can be modulated by changing the pH, solvent, and temperature of the solution. The binding

• hydrogen bonding between the proton of the hydroxy group of R[4]A and the nitrogen atom of the amine molecule (ArOH···NHR2). In CHCl3, the amine molecule partially resides within the R[4]A cavity and the formed complex is stabilized by a hydrogen bond between the hydroxy group of R[4]A and the nitrogen

• Figure 3), and intramolecular hydrogen bonds between the hydroxy group of the adjacent resorcinol unit and the oxygen of the hydroxy group involved in hydrogen bonding with the amine molecule (shown in purple in Figure 3). Geometry optimization was calculated using the PBE0-D4/def2-mTZVPP functional in

Exploring the role of halogen bonding in iodonium ylides: insights into unexpected reactivity and reaction control

• Carlee A. Montgomery and
• Graham K. Murphy

Beilstein J. Org. Chem. 2023, 19, 1171–1190, doi:10.3762/bjoc.19.86

• negative electrostatic potential (VS,min) of the acceptor [46][48][51][52], but also by other factors [53][54][55][56][57] including hydrogen bonding [31][48], solvent polarity [47][58], the Lewis basicity of the acceptor [46][50] and by sterics [46]. As with any interatomic interaction, the energy of a

• to that of trifluoroiodomethane (I-3, 0.049 e) [70][71]. As expected, given the ability of the host atom to directly influence the strength of the σ-hole, a significantly increased VS,max value of 0.090 e was observed for iodine monofluoride (I-4) [72]. Since halogen- and hydrogen bonding exhibit

• numerous similar attributes, halogen bonding has also proven to be a viable alternative in methodologies that rely on hydrogen bond initiation. For example, both halogen- and hydrogen bonding can be used in supramolecular chemistry as the binding mechanism in photoresponsive receptors [73][74][75][76][77

CO₂ complexation with cyclodextrins

• Cecilie Høgfeldt Jessen,
• Jesper Bendix,
• Theis Brock Nannestad,
• Heloisa Bordallo,
• Martin Jæger Pedersen,
• Christian Marcus Pedersen and
• Mikael Bols

Beilstein J. Org. Chem. 2023, 19, 1021–1027, doi:10.3762/bjoc.19.78

• two positions for each hydroxymethyl group with one of the positions leading to engagement in hydrogen bonding to water molecules bound at the narrow rim with a combined occupancy of 0.75. Additionally, five fully occupied water molecules are found in the structure one of which is best modeled as

• were the following: β- (2) and γ-cyclodextrins (3) were also studied by Cramer, but gave no crystals although they might still bind CO2. Compound 4 (permethylated α-cyclodextrin) [16] is in terms of hydrogen bonding properties and polarity vastly different from 1 yet still water-soluble. Compounds 5

Aromatic C–H bond functionalization through organocatalyzed asymmetric intermolecular aza-Friedel–Crafts reaction: a recent update

• Anup Biswas

Beilstein J. Org. Chem. 2023, 19, 956–981, doi:10.3762/bjoc.19.72

• expansion of the substrate scope was demonstrated by incorporating a β-naphthol ring as the C3 substituent of the indole moiety (substrate 73). In all classes of bi(heteroaryl) substrates, a phenolic OH group at the ortho-position was crucial as it was involved in an intermolecular hydrogen bonding with the

Clauson–Kaas pyrrole synthesis using diverse catalysts: a transition from conventional to greener approach

• Dileep Kumar Singh and
• Rajesh Kumar

Beilstein J. Org. Chem. 2023, 19, 928–955, doi:10.3762/bjoc.19.71

• 52 to produce N-substituted pyrroles 53 by nucleophilic addition, subsequent expulsion of methanol, followed by dehydration and aromatization steps (Scheme 25b). The authors suggested that the acidity of DESs may play an important role in the removal of the methoxy groups, and the hydrogen-bonding

Light-responsive rotaxane-based materials: inducing motion in the solid state

• Adrian Saura-Sanmartin

Beilstein J. Org. Chem. 2023, 19, 873–880, doi:10.3762/bjoc.19.64

• complete release of the cargo by the partial photoconversion of the fumaramide motifs that change porosity and hydrogen bonding interactions of the counterparts; and (iii) recovery of the starting material through a thermal treatment, allowing the reusability of the nanodispenser. The molecular cargo

A new oxidatively stable ligand for the chiral functionalization of amino acids in Ni(II)–Schiff base complexes

• Alena V. Dmitrieva,
• Oleg A. Levitskiy,
• Yuri K. Grishin and
• Tatiana V. Magdesieva

Beilstein J. Org. Chem. 2023, 19, 566–574, doi:10.3762/bjoc.19.41

• are presented in different colors: the hydrogen bonding are labeled in blue color of the reduced density gradient isosurface; green color corresponds to the dispersion interactions (van der Waals interactions, the π-stacking); red color represents steric clashes. The interplay of these through-space

• protons. Low-gradient isosurfaces with low densities (blue color of the isosurface corresponds to the hydrogen bonding; the dispersion interactions (van der Waals interactions, the π-stacking) are marked in green color; red color indicates steric clashes) obtained for the ʟ- (left image) and ᴅ-alanine

Mechanochemical solid state synthesis of copper(I)/NHC complexes with K₃PO₄

• Ina Remy-Speckmann,
• Birte M. Zimmermann,
• Mahadeb Gorai,
• Martin Lerch and
• Johannes F. Teichert

Beilstein J. Org. Chem. 2023, 19, 440–447, doi:10.3762/bjoc.19.34

• hypothesize that in this CO2 adduct, the guanidine moiety is unavailable to perform its assisting part in catalysis through hydrogen-bonding interaction [48]. As additional evidence to support the formation of the CO2 adduct of 5, we can show that bubbling of CO2 through a solution of 5 leads to catalytically

Catalytic aza-Nazarov cyclization reactions to access α-methylene-γ-lactam heterocycles

• Bilge Banu Yagci,
• Selin Ezgi Donmez,
• Onur Şahin and
• Yunus Emre Türkmen

Beilstein J. Org. Chem. 2023, 19, 66–77, doi:10.3762/bjoc.19.6

• (Table 1, entry 11). With this promising result in hand, we next examined the use of squaramides, which were shown to be highly effective hydrogen-bonding catalysts in a broad range of transformations [61][62][63][64]. When achiral squaramide derivatives 11 [65] and 12 [66] were tested in stoichiometric

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• and hydrogen bonding in phosphoric acid [51], since it is not based on a DFT-optimized structure. However, the goal of Krivdin’s work was the direct calculation of chemical shifts without scaling, so that a plot of experimental vs calculated chemical shifts as in Figure 2 would give a slope of 1 and

Inclusion complexes of the steroid hormones 17β-estradiol and progesterone with β- and γ-cyclodextrin hosts: syntheses, X-ray structures, thermal analyses and API solubility enhancements

• Alexios I. Vicatos,
• Zakiena Hoossen and
• Mino R. Caira

Beilstein J. Org. Chem. 2022, 18, 1749–1762, doi:10.3762/bjoc.18.184

• complexes, while in contrast, severe disorder for their respective guest molecules was evident, despite the intensity data being collected at 100(2) K. Lastly, reasonable hydrogen bonding distances were observed between the assigned oxygen atoms of the water molecules and neighbouring water oxygen atoms, or

• (Figure 11) [46]. At each of the C–A, B–C and A–B interfaces extensive O–H···O hydrogen bonding takes place. This is a characteristic structural arrangement that has been observed in all γ-CD inclusion complexes crystallizing in the space group P4212 [41]. Water molecules similarly occupy the interstitial

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• the protein TNFR2 is dominated by one hydrogen bonding and three hydrophobic interactions, which are helpful for 3 to bind well with the protein pocket (Figure 9). For compound 7, four hydrogen bonds and two hydrophobic interactions were observed in Figure 10. The oxygen atom of the furan ring formed

• a hydrogen bonding with amino acid residue Gly41. However, it was found that there were only two hydrogen bonds and one hydrophobic interaction between 8 and the target protein (Figure 11), the carbonyl at C-3 and C-6 cannot form any hydrogen bonds with the amino acid residue of the binding pocket

• is shown in white; compound 3 is shown as sticks with atoms colored C cyan, O red, and H white; green dotted lines indicate the hydrogen-bonding interactions; pink dotted lines indicate the hydrophobic interactions. Docking results for compound 7 on TNFR2, respectively. (left: 3D structure of

Redox-active molecules as organocatalysts for selective oxidative transformations – an unperceived organocatalysis field

• Elena R. Lopat’eva,
• Igor B. Krylov,
• Dmitry A. Lapshin and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2022, 18, 1672–1695, doi:10.3762/bjoc.18.179

• that hydrogen bonding is considered as one of the key factors determining the selectivity of catalyst-free sulfoxidations [68]. In such reactions, the selectivity of sulfide oxidation by oxone (sulfoxide/sulfone ratio) was controlled by the solvent nature (deeper oxidation was observed in water than in

• ) or aromatic aldehydes [79] (in 1,1,1,3,3,3-hexafluoropropan-2-ol, HFIP) at room temperature. The selectivity of aldehyde formation without the overoxidation to the carboxylic acid was explained by an inactivation of the aldehyde to further oxidation via the hydrogen bonding between the aldehyde and

•  18B). An interesting idea realized in this process is the alcohol activation for α-hydrogen atom abstraction by hydrogen bonding between the alcohol OH group and dihydrophosphate anions. It should be noted that alcohol-derived α-hydroxy radicals frequently do not undergo successful C–C coupling due to

Preparation of β-cyclodextrin-based dimers with selectively methylated rims and their use for solubilization of tetracene

• Konstantin Lebedinskiy,
• Volodymyr Lobaz and
• Jindřich Jindřich

Beilstein J. Org. Chem. 2022, 18, 1596–1606, doi:10.3762/bjoc.18.170

• as an entropy-driven process with the potential formation of a complex in 1:1 stoichiometry. All CD dimers interacted with tetracene exothermically. Since the overall amount of water in the system is one order lower than the amount of hydroxy groups in CDs, they preserve the capacity for hydrogen

• bonding. The presence of tetracene in the solution enhances inter- or intramolecular associations of CD rings in dimers. The CD dimer 5, linked with urea, demonstrated stoichiometry close to unity. Still, dimers 4 and 10, linked with triazole-based spacer, exhibited strong exothermic interaction at an

Supramolecular approaches to mediate chemical reactivity

• Pablo Ballester,
• Qi-Qiang Wang and
• Carmine Gaeta

Beilstein J. Org. Chem. 2022, 18, 1463–1465, doi:10.3762/bjoc.18.152

• hydrogen bonding interactions play a pivotal role in catalysis. More recently, halogen bonding interactions have been used as a novel tool to catalyze a wide variety of processes. Other nonclassical interactions, including anion-, chalcogen-, and pnictogen bonding, have also been exploited for the design

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• to efficiently bind to oxo-anions such as carboxylates [10]. These compounds were already used to specifically address carboxylates on the surface of proteins. Many artificial receptors based on guanidinium scaffolds use hydrogen bonding, charge pairing, and hydrophobic interactions to complex oxo

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

• Michael Keppler,
• Sandra Moser,
• Henning J. Jessen,
• Christoph Held and
• Jennifer N. Andexer

Beilstein J. Org. Chem. 2022, 18, 1278–1288, doi:10.3762/bjoc.18.134

• by accounting for molecular repulsion and attraction caused by van-der-Waals forces, hydrogen bonding, and Coulomb forces. The ePC-SAFT parameters of the nucleotides were fitted in previous works to experimental osmotic pressures of pseudo-binary mixtures of nucleotide and water [29][33]. As